When any part of the contents become removed (even if replaced immediately) the map icon colour changes to green and a mouse-over will only glean the PDA description "Stash". This also occurs if an item is added to the contents and then removed.

Locations that are known to be stash locations but are empty (because the coordinates have not yet been obtained) may be used by the player to store items on a non-volatile basis and will have the contents added to with the appropriate loot if the coordinates are subsequently obtained.

This is just loot that is scripted to appear on the map in the ordinary course of the game without an external container. An example might be a Bandit jacket with a Cmuphob vodka bottle on a Rostok building site.